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Yorodumi- PDB-8e7m: Structure of the human ACE2 receptor in complex with antibody Fab... -
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-Basic information
Entry | Database: PDB / ID: 8e7m | ||||||
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Title | Structure of the human ACE2 receptor in complex with antibody Fab fragment, 05B04 | ||||||
Components |
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Keywords | ANTIVIRAL PROTEIN / ACE2 / antibody / SARS-CoV-2 / inhibition | ||||||
Function / homology | Function and homology information positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / carboxypeptidase activity / negative regulation of signaling receptor activity / Attachment and Entry / positive regulation of cardiac muscle contraction / regulation of cytokine production / viral life cycle / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / regulation of transmembrane transporter activity / cilium / negative regulation of ERK1 and ERK2 cascade / positive regulation of reactive oxygen species metabolic process / metallopeptidase activity / endocytic vesicle membrane / regulation of cell population proliferation / virus receptor activity / regulation of inflammatory response / endopeptidase activity / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / entry receptor-mediated virion attachment to host cell / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / receptor-mediated virion attachment to host cell / symbiont entry into host cell / apical plasma membrane / membrane raft / endoplasmic reticulum lumen / cell surface / extracellular space / extracellular exosome / zinc ion binding / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Barnes, C.O. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biorxiv / Year: 2022 Title: Human anti-ACE2 monoclonal antibodies as pan-sarbecovirus prophylactic agents Authors: Zhang, F. / Jenkins, J. / de Carvalho, R.V. / Nakandakari-Higa, S. / Chen, T. / Abernathy, M.E. / Nyakatura, E. / Andrew, D. / Lebedeva, I. / Lorenz, I.C. / Hoffmann, H.H. / Rice, C.M. / ...Authors: Zhang, F. / Jenkins, J. / de Carvalho, R.V. / Nakandakari-Higa, S. / Chen, T. / Abernathy, M.E. / Nyakatura, E. / Andrew, D. / Lebedeva, I. / Lorenz, I.C. / Hoffmann, H.H. / Rice, C.M. / Victora, G.D. / Barnes, C.O. / Haziioannou, T. / Bieniasz, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8e7m.cif.gz | 201.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8e7m.ent.gz | 154.3 KB | Display | PDB format |
PDBx/mmJSON format | 8e7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8e7m_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8e7m_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8e7m_validation.xml.gz | 48.1 KB | Display | |
Data in CIF | 8e7m_validation.cif.gz | 69.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/8e7m ftp://data.pdbj.org/pub/pdb/validation_reports/e7/8e7m | HTTPS FTP |
-Related structure data
Related structure data | 27939MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 72306.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) References: UniProt: Q9BYF1, angiotensin-converting enzyme 2, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases |
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-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 23948.818 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human) |
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#3: Antibody | Mass: 23549.191 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human) |
-Sugars , 3 types, 6 molecules
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | |
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-Details
Has ligand of interest | N |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: hACE2 + 05B04 Fab fragment / Type: COMPLEX Details: Complex between soluble ACE2 bound to 05B04 Fab fragment Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Value: .1 MDa / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: Expi293 |
Buffer solution | pH: 8 |
Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.6 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6599 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2055266 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 490485 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 112 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: CC | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6VW1 Accession code: 6VW1 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.2 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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